CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

Abstract

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle

“…Unknown taxa and misidentified genes may be playing key roles in ecological and metabolic processes but researchers are unable to confidently identify them, let alone make statements about their importance in a microbial ecology 35 . Recent human gut microbiome metagenome studies from diverse populations will undoubtedly improve database representation but the number of studies and metagenomic samples from non-industrial populations still pales in comparison to industrial gut microbiomes 26 , 35 , 37 , 38 .…”

“…OU IRB deemed this project consistent with US policy 45 CFR 46.101(b) exempt category 4 (OU IRB 6976). Gut metagenomic data were generated as given in Borry et al 37 . All experiments were performed in accordance with relevant guidelines and regulations, with the University of Oklahoma Institutional Biosafety Committee approving the chemical assays (IBC #1044).…”

Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus

“…Additionally, host DNA content may leach between coprolites, as well as other sources [ 115 ]. Fortunately, recently developed bioinformatic approaches are improving our ability to distinguish human from non-human coprolites [ 57 , 116 ]. Finally, coprolites are relatively delicate and often expose the sample to processes that alter DNA sequences and fragment nucleic acids.…”

Coprolite research: archaeological and paleoenvironmental potentials

“…Perhaps the most important takeaway of the Reinhard et al paper is the conclusion that the condition of microremains observed in SEM provide insight into the overall organic preservation in coprolites that can be used to assess whether the sample should be prioritized for biomolecular analysis. These results are particularly useful with the move towards increasing biomolecular analytical techniques (e.g., aDNA) (Battillo and Fisher 2015;Borry et al 2020;Shillito et al 2020a). These methods have limited utility in some coprolites, hypothesized to be the results of taphonomic processes that result in poor aDNA preservation.…”